The Magus is Adam Warlock's future self, in a timeline where he has turned out to be quite the villain. He got to be this way because the Magus would come back from the future, beat up his younger self, then give him to the In-Betweener to be worked over for centuries by Lord Chaos and Master Order until it was inevitable that he become the Magus. (Aren't time loops fun?) He has all the powers of Adam Warlock, as well as his soul gem.

So the Magus had never existed...until Adam Warlock got a hold of the Infinity Gauntlet and effectively became God. To ensure infallibility, he expelled all good and evil from himself. The evil side became the Magus. This time, the Magus was just a shade of Adam Warlock, but he was extremely crafty. Through a series of manipulations, the Magus gained the Infinity Gauntlet. (This was in The Infinity War.) However, the reality gem was a fake, and so ultimate power was not his. He was promptly absorbed into the soul gem. A power-stealing villain named Siphonn (or some such thing) stole the soul gem from Warlock for a brief period of time. Because Siphonn did not have the same degree of control over the gem as Warlock did, the Magus was able to escape before Warlock reclaimed the gem. Lately, the Magus has been harassing the new Captain Marvel, using new power-stealing abilities he picked up from Siphonn.

This plan was interrupted, however, by Crono and his friends. They barged in on Magus in the middle of the summoning, and forced Magus to devote some of his attention to them. Magus still managed to call Lavos, who again opened a variety of gates, sending Magus back into the Dark Ages.

On the subject of Chrono Trigger, an interesting note on Magus's name: in the original Japanese, Magus went by Maou, which meant "demonking". The Mystics, naturally enough, were called Mazoku ("demonrace/tribe"). Also, Magus's given name, Janus, was Jaki in the Japanese version, which was a pun on "evil aura".

All of which makes Magus slightly more sinister (as if he needed any help...).